Figure 1 Multiple alignment of sequences corresponding to the region between the degenerate primers  

MSV-CT     CAGAAGCCTAGGGGTTCATAATTACTGGCAAAATAATGTTGATTGGTCTTC---ATACAA
MSV-Dig    CAGAAGCTTAGGGCTTCATAATTATTGGCAAAATAATGTTGATTGGTCTTC---GTACAA
MSV-Kom    CAGAAGCCTAGGGGTTCATAATTACTGGCAAAATAATGTTGATTGGTCTTC---ATACAA
MSV-RSE    CAGAAGCCTAGGGGTTCATAATTACTGGCAAAATAATGTTGATTGGTCTTC---ATACAA
MSV-Set    TAGAAGCTTAGGGCGTCATAATTACTGGCAAAA---TGTTGATTGGTCTTC---CTACAA
MSV-Tas    CAGAAGCTTAGGGCTTCATAATTATTGGCAAAATAATGTTGATTGGTCTTC---TTACAA
MSV-VW     CAGAAGCTTAGGGCTTCATAATTATTGGCAAAATAATGTTGATTGGTCTTC---GTACAA
MSV-VM     CAGAAGCCTAGGGGTTCATAATTACTGGCAAAATAATGTTGATTGGTCTTC---ATACAA
MSV-WES    -----GCTTAGGGCTTCATAATTATTGGCAAAATAATGTTGATTGGTCTTC---GTACAA
MSV-K      CAGAAGCCTAGGGGTTCATAATTACTGGCAAAATAATGTTGATTGGTCTTC---ATACAA
MSV-N      CAGAAGCCTAGGGGTTCATAATTACTGGCAAAATAATGTTGATTGGTCTTC---ATACAA
MSV-Reu    CAGAAGCCTAGGGGTTCATAATTACTGGCAAAATAATGTTGATTGGTCTTC---ATACAA
MSV-S      CAGAAGCCTAGGGGTTCATAATTACTGGCAAAATAATGTTGATTGGTCTTC---ATACAA
CSMV-C     CAGAAGTCTTGGAACTCATCACTACTGGCAGCACTCAGTGAACTTCCTAGAGGAATGGAA
CSMV       CAGAAGTCTTGGAACTCATCACTACTGGCAGCACTCAGTGAACTTCCTAGAGGAATGGAA
DSV        CAGAGGGCTAGGTAGACATAATTACTGGCAAAATAATGTAGACTGGGCTTC---TTATGA
PanSV-Ken  TAGAAGCCTCGGACGACACAACTACTGGCAAAACAATATCGACTGGTCTTC---ATATGA
SSV-M      CCGTAGCCTGGGAAGACATAATTACTGGCAAAACAACGTCGACTGGTCCTG---CTACGA
SSV-N      CAGGAGCCTGGGAAGACATAATTACTGGCAGAACAACGTCGACTGGTCCTC---CTACGA
MiSV       CAGAAACATCGGGAGGCACAACTACTACAACTCAACCGTAGACTTCACACA---CTATGA
WDV        AAGGTCTCTAGGGACACACAATTATTATAACAGTCTAGTTGATTTCACAAC---ATATGA
                   * **    **  * ** *   *        *  * *           *   *

MSV-CT     CGAAGACGCAATCTACAACATCGTAGATGATATTCCGTTTAAATTCTGTCCTTGTTGGAA
MSV-Dig    CGAAGACGCAATCTACAACATCGTAGATGACATTCCTTTTAAATTCTGTCCTTGTTGGAA
MSV-Kom    CGAAGACGCAATCTACAACATCGTAGATGATATTCCGTTTAAATTCTGTCCTTGTTGGAA
MSV-RSE    CGAAGACGCAATCTACAACATCGTAGATGATATTCCGTTTAAATTCTGTCCTTGTTGGAA
MSV-Set    CGAAGACACAATCTACAACATCGTAGATGATATCCCCTTTAAATATTGTCCTTGCTGGAA
MSV-Tas    CGAAGACGCAATCTACAACATCGTAGATGATATTCCATTTAAATTCTGTCCTTGTTGGAA
MSV-VW     CGAAGACGCAATCTACAACATCGTAGATGATATTCCTTTTAAATTCTGTCCTTGTTGGAA
MSV-VM     CGAAGACGCAATCTACAACATCGTAGATGATATTCCGTTTAAATTCTGTCCTTGTTGGAA
MSV-WES    CGAAGACGCAATCTACAACATCGTAGATGATATTCCTTTTAAATTCTGTCCTTGTTGGAA
MSV-K      CGAACACGCAATCTACAACATCGTAGATGATATTCCGTTTAAATTCTGTCCTTGTTGGAA
MSV-N      CGAAGACGCAATCTATAACATCGTAGATGATATTCCGTTTAAATTCTGTCCTTGTTGGAA
MSV-Reu    CGAAGACGCAATCTACAACATCGTAGACGATATTCCATTTAAATTCTGTCCTTGTTGGAA
MSV-S      CGAAGACGCAATCTACAACATCGTAGATGATATTCCGTTTAAATTCTGTCCTTGTTGGAA
CSMV-C     CTGCCAGGCCCAGTTCAACATCATTGATGACATCCCGTTCAAGTTCGTCCCTTGTTGGAA
CSMV       CTGCCAGGCCCAGTTCAACATCATTGATGACATCCCGTTCAAGTTCGTCCCTTGTTGGAA
DSV        CGAGGAAGCCCAGTTCAATGTCATTGATGACATACCATTCAAGTTCTGTCCTTGTTGGAA
PanSV-Ken  TGAAGAAGCTCAGTACAATGTCGTTGACGACATTCCCTTCAAGTTCTGTCCGTGCAGGAA
SSV-M      CGAGGACGCAGTCTACAACGTCATTGACGACATCCCCTTCAAGTTCTGTCCTTGCTGGAA
SSV-N      CGAGGACGCAGAATACAACATCATCGACGACATACCCTTCAAGTACTGTCCATGCTGGAA
MiSV       CAAAGATGCAATCTACAACGTCATCGACGATGTGCCTTTCAAGTTCTTGCCGCAGTGGAA
WDV        CGTCAACGCCAAGTATAATATCATCGACGACATTCCATTCAAGTTCACACCCAACTGGAA
                *  *    *  **  ** * ** **  * ** ** ** *     **     ****

MSV-CT     ACAGTTAGTTGGCTGCCAGAGGGATTTCATTGTAAACCCCAAGTATGGTAAGAAGAAAAA
MSV-Dig    ACAGTTAGTTGGCTGTCAGAAAGAGTTCGTGGTAAATCCAAAATATGGCAAGAAGAAGAA
MSV-Kom    ACAGTTAGTTGGCTGTCAGAGGGATTTCATTGTAAACCCCAAGTATGGTAAGAAGAAAAA
MSV-RSE    ACAGTTAGTTGGCTGTCAGAGGGATTTCATTGTAAACCCCAAGTATGGTAAGAAGAAAAA
MSV-Set    ACAGTTGGTTGGCTGTCAAAAAGAATTCGTTGTAAATCCTAAATACGGGAAGAAGAAGAA
MSV-Tas    ACAGTTAGTTGGCTGTCAGAAAGAGTTCGTTGTAAATCCAAAATATGGCAAGAAGAAGAA
MSV-VW     ACAGTTAGTTGGCTGTCAGAAAGAGTTCGTGGTAAATCCAAAATATGGCAAGAAGAAGAA
MSV-VM     ACAGTTAGTTGGCTGTCAGAGGGATTTCATTGTAAACCCCAAGTATGGTAAGAAGAAAAA
MSV-WES    ACAGTTAGTTGGCTGTCAGAAAGAGTTCGTGGTAAATCCAAAATATGGCAAGAAGAAGAA
MSV-K      ACAGTTAGTTGGCTGTCAGAGGGATTTCATTGTAAACCCCAAATATGGTAAGAAGAAGAA
MSV-N      ACAGTTAGTTGGCTGTCAGAGGGATTTCATTGTAAACCCCAAGTATGGTAAAAAGAAAAA
MSV-Reu    ACAGTTAGTTGGCTGCCAGAAAGATTTCATTGTCAACCCCAAGTATGGTAAGAAGAAGAA
MSV-S      ACAGTTAGTTGGCTGTCAGAGGGATTTCATTGTAAACCCCAAGTATGGTAAGAAGAAAAA
CSMV-C     GGGACTCGTCGGCAGCCAGTATGACCTGACGGTAAACCCCAAGTACGGGAAGAAGAAAAG
CSMV       GGGACTCGTCGGCAGCCAGTATGACCTGACGGTAAACCCCAAGTACGGGAAGAAGAAAAG
DSV        ACAGTTGATTGGTTGTCAGAAAGAATACGTCGTCAACCCTAAGTATGGTAAAAAGAAGCN
PanSV-Ken  ACGACTCGTCGGCTGCCAAAAAGACTACATAGTCAATCCCAAGTACGGGAAACGCCGGAA
SSV-M      GCAACTGATTGGTTGCCAAGAGAACTACGTCGTTAATCCCAAGTATGGGAAGAAACGGAG
SSV-N      GCAACTGATTGGCTGCCAGAAGGATTATATTGTAAATCCAAAGTACGGCAAGCGTAAGAA
MiSV       GGCGCTGGTGGGAGCACAGCGTGACTACATAGTGAATCCCAAGTACGGTAA---GAAGAA
WDV        GTGCTTCGTCGGGGCTCAGCGTGACTTCACGGTCAATCCAAAATATGGTAA---GCGAAA
                *  * **    **     *       ** ** ** ** ** ** **

MSV-CT     GGTGCAGAAGAAGTGTAAGCCATCAATAATCCTCGCCAACT
MSV-Dig    AGTTCAGATGAAGTCTAAGCCTACAATCATCCTCGCCAACT
MSV-Kom    GGTGCAGAAGAAGTCTAAGCCTACAATAATCCTCGCCAACT
MSV-RSE    GGTGCAGAAGAAGTCTAAGCCTACAATAATCCTCGCCAACT
MSV-Set    GGTTCAGATGAAGTCTAAACCTACTATCATTCTCGCCAACT
MSV-Tas    AGTTCAGATGAAGTCTAAGCCTACAATCATCCTCGCCAACT
MSV-VW     AGTTCAGATGAAGTCTAAGCCTACAATCATCCTCACCAACT
MSV-VM     GGTGCAGAAGAAGTCTAAGCCTACAATAATCCTCGCCAACT
MSV-WES    AGTTCAGATGAAGTCTAAGCCTACAATCATCCTCGCCAACT
MSV-K      GGTGCACAAGAAGTCTAAGCCTACAATAATCCTCGCCAACT
MSV-N      GGTGCAGAAGAAGTCTAAGCCTACAATAATCCTCGCCAACT
MSV-Reu    GGTGCAGAAGAAGTCTAAGCCTACAATAATCCTCGCCAACT
MSV-S      GGTGCAGAAGAAGTCTAAGCCTACAATAATCCTCGCCAACT
CSMV-C     AATCCCCA---ACGGGATTCCGTGTATTATACTCGTGAACG
CSMV       AATCCCCA---ACGGGATTCCATGTATTATCCTCGTAAACG
DSV        TGTTGCTTCTAAATCCATACCATCAATAATCCTCACCAATC
PanSV-Ken  GGTAGCATCCAAGAGCATTCCAACTATCATCCTCGCCAACG
SSV-M      AGTAGCCAAGAAAAGCATCTCCACAATTGTTCTTGCCAACG
SSV-N      AGTAGCTAGTAAATCCATCCCCACTATAGTGCTAGCCAATG
MiSV       GAAAATCCCTGGGGGAATCCCGTCCATCATTCTAACCAATG
WDV        GGTCATACGGGGTGGAATACCTTGCATCATTTTAGTTAATC
                           *   *    **  *  *    **

  Legend:

Sequences aligned using DNAMAN ver. 3.0; output according to CLUSTAL format. Dashes indicate gaps inserted to maximise alignment, red asterisks indicate conserved bases. Sequences of 218 bases (excluding gaps) were compared: these were truncated from the sequenced +/-254 bp PCR products by removal of the primer sequences (34 bp) and of an additional 2 bases. Sequences determined in this work are in blue. See Table 1 for sequence designations.